How to use the parmed.Atom function in ParmEd

def mol_to_parmed(mol):
    """ Convert MDT Molecule to parmed Structure
    Args:
        mol (moldesign.Molecule):

    Returns:
        parmed.Structure
    """
    import parmed
    struc = parmed.Structure()
    struc.title = mol.name

    pmedatoms = []
    for atom in mol.atoms:
        pmedatm = parmed.Atom(atomic_number=atom.atomic_number,
                              name=atom.name,
                              mass=atom.mass.value_in(u.dalton),
                              number=utils.if_not_none(atom.pdbindex, -1))
        pmedatm.xx, pmedatm.xy, pmedatm.xz = atom.position.value_in(u.angstrom)
        pmedatoms.append(pmedatm)
        struc.add_atom(pmedatm,
                       resname=utils.if_not_none(atom.residue.resname, 'UNL'),
                       resnum=utils.if_not_none(atom.residue.pdbindex, -1),
                       chain=utils.if_not_none(atom.chain.name, ''))

    for bond in mol.bonds:
        struc.bonds.append(parmed.Bond(pmedatoms[bond.a1.index],
                                       pmedatoms[bond.a2.index],
                                       order=bond.order))
    return struc

def createStructureFromResidue(residue):
    # Create ParmEd structure for residue.
    structure = parmed.Structure()
    for a in residue.atoms():
        if a.element is None:
            atom = parmed.ExtraPoint(name=a.name)
        else:
            atom = parmed.Atom(atomic_number=a.element.atomic_number, name=a.name, mass=a.element.mass)
        structure.add_atom(atom, residue.name, residue.index, 'A')
        atommap[a] = atom
    for a1, a2 in topology.bonds():
        structure.bonds.append(Bond(atommap[a1], atommap[a2]))

    return structure